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European Journal of Human Genetics: EJHG

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https://www.readbyqxmd.com/read/30659262/reply-to-bombard-and-mighton
#1
LETTER
Daniele Carrieri, Heidi C Howard, Angus J Clarke, Vigdis Stefansdottir, Martina C Cornel, Carla G van El, Francesca Forzano
No abstract text is available yet for this article.
January 18, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30659261/enriched-power-of-disease-concordant-twin-case-only-design-in-detecting-interactions-in-genome-wide-association-studies
#2
Weilong Li, Jan Baumbach, Afsaneh Mohammadnejad, Charlotte Brasch-Andersen, Fabio Vandin, Jan O Korbel, Qihua Tan
Genetic interaction is a crucial issue in the understanding of functional pathways underlying complex diseases. However, detecting such interaction effects is challenging in terms of both methodology and statistical power. We address this issue by introducing a disease-concordant twin-case-only design, which applies to both monozygotic and dizygotic twins. To investigate the power, we conducted a computer simulation study by setting a series of parameter schemes with different minor allele frequencies and relative risks...
January 18, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30659260/biallelic-intragenic-duplication-in-adgrb3-bai3-gene-associated-with-intellectual-disability-cerebellar-atrophy-and-behavioral-disorder
#3
Carmela Scuderi, Lucia Saccuzzo, Mirella Vinci, Lucia Castiglia, Ornella Galesi, Michele Salemi, Teresa Mattina, Eugenia Borgione, Santina Città, Corrado Romano, Marco Fichera
In recent years, chromosomal microarray analysis has permitted the discovery of rearrangements underlying several neurodevelopmental disorders and still represents the first diagnostic test for unexplained neurodevelopmental disabilities. Here we report a family of consanguineous parents showing psychiatric disorders and their two sons both affected by intellectual disability, ataxia, and behavioral disorder. SNP/CGH array analysis in this family demonstrated in both siblings a biallelic duplication inherited from the heterozygous parents, disrupting the ADGRB3 gene...
January 18, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30659259/genetic-basis-for-plasma-amino-acid-concentrations-based-on-absolute-quantification-a-genome-wide-association-study-in-the-japanese-population
#4
Akira Imaizumi, Yusuke Adachi, Takahisa Kawaguchi, Koichiro Higasa, Yasuharu Tabara, Kazuhiro Sonomura, Taka-Aki Sato, Meiko Takahashi, Toshimi Mizukoshi, Hiro-O Yoshida, Naoko Kageyama, Chisato Okamoto, Mariko Takasu, Maiko Mori, Yasushi Noguchi, Nobuhisa Shimba, Hiroshi Miyano, Ryo Yamada, Fumihiko Matsuda
To assess the use of plasma free amino acids (PFAAs) as biomarkers for metabolic disorders, it is essential to identify genetic factors that influence PFAA concentrations. PFAA concentrations were absolutely quantified by liquid chromatography-mass spectrometry using plasma samples from 1338 Japanese individuals, and genome-wide quantitative trait locus (QTL) analysis was performed for the concentrations of 21 PFAAs. We next conducted a conditional QTL analysis using the concentration of each PFAA adjusted by the other 20 PFAAs as covariates to elucidate genetic determinants that influence PFAA concentrations...
January 18, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30651584/a-genetic-perspective-on-longobard-era-migrations
#5
Stefania Vai, Andrea Brunelli, Alessandra Modi, Francesca Tassi, Chiara Vergata, Elena Pilli, Martina Lari, Roberta Rosa Susca, Caterina Giostra, Luisella Pejrani Baricco, Elena Bedini, István Koncz, Tivadar Vida, Balázs Gusztáv Mende, Daniel Winger, Zuzana Loskotová, Krishna Veeramah, Patrick Geary, Guido Barbujani, David Caramelli, Silvia Ghirotto
From the first century AD, Europe has been interested by population movements, commonly known as Barbarian migrations. Among these processes, the one involving the Longobard culture interested a vast region, but its dynamics and demographic impact remains largely unknown. Here we report 87 new complete mitochondrial sequences coming from nine early-medieval cemeteries located along the area interested by the Longobard migration (Czech Republic, Hungary and Italy). From the same areas, we sampled necropoleis characterized by cultural markers associated with the Longobard culture (LC) and coeval burials where no such markers were found, or with a chronology slightly preceding the presumed arrival of the Longobards in that region (NLC)...
January 16, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30626931/inverse-pcr-to-perform-long-distance-haplotyping-main-applications-to-improve-preimplantation-genetic-diagnosis-in-hemophilia
#6
Miguel Martín Abelleyro, Vanina Daniela Marchione, Micaela Palmitelli, Claudia Pamela Radic, Daniela Neme, Irene Beatriz Larripa, Enrique Medina-Acosta, Carlos Daniel De Brasi, Liliana Carmen Rossetti
Among other applications of long-distance haplotype phasing in clinical genetics, determination of linked DNA markers as surrogate for problematic structural variants (e.g., repeat-mediated rearrangements) is essential to perform diagnosis from low-quality DNA samples. We describe a next-of-kin-independent (physical) phasing approach based on inverse-PCR (iPCR) paired-end amplification (PI). This method enables typing the multialleles of the short tandem repeat (STR) F8Int21[CA]n at the F8-intron 21, as a surrogate DNA marker for the F8-intron 22 inversion (Inv22), the hemophilia A-causative hotspot, within the transmitted haplotype in informative carriers...
January 9, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30626930/value-of-genetic-analysis-for-confirming-inborn-errors-of-metabolism-detected-through-the-spanish-neonatal-screening-program
#7
Rosa Navarrete, Fátima Leal, Ana I Vega, Ana Morais-López, María Teresa Garcia-Silva, Elena Martín-Hernández, Pilar Quijada-Fraile, Ana Bergua, Inmaculada Vives, Inmaculada García-Jiménez, Raquel Yahyaoui, Consuelo Pedrón-Giner, Amaya Belanger-Quintana, Sinziana Stanescu, Elvira Cañedo, Oscar García-Campos, María Bueno-Delgado, Carmen Delgado-Pecellín, Isidro Vitoria, María Dolores Rausell, Elena Balmaseda, Mari Luz Couce, Lourdes R Desviat, Begoña Merinero, Pilar Rodríguez-Pombo, Magdalena Ugarte, Celia Pérez-Cerdá, Belén Pérez
The present work describes the value of genetic analysis as a confirmatory measure following the detection of suspected inborn errors of metabolism in the Spanish newborn mass spectrometry screening program. One hundred and forty-one consecutive DNA samples were analyzed by next-generation sequencing using a customized exome sequencing panel. When required, the Illumina extended clinical exome panel was used, as was Sanger sequencing or transcriptional profiling. Biochemical tests were used to confirm the results of the genetic analysis...
January 9, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30626929/rapid-and-accurate-interpretation-of-clinical-exomes-using-phenoxome-a-computational-phenotype-driven-approach
#8
Chao Wu, Batsal Devkota, Perry Evans, Xiaonan Zhao, Samuel W Baker, Rojeen Niazi, Kajia Cao, Michael A Gonzalez, Pushkala Jayaraman, Laura K Conlin, Bryan L Krock, Matthew A Deardorff, Nancy B Spinner, Ian D Krantz, Avni B Santani, Ahmad N Abou Tayoun, Mahdi Sarmady
Clinical exome sequencing (CES) has become the preferred diagnostic platform for complex pediatric disorders with suspected monogenic etiologies. Despite rapid advancements, the major challenge still resides in identifying the casual variants among the thousands of variants detected during CES testing, and thus establishing a molecular diagnosis. To improve the clinical exome diagnostic efficiency, we developed Phenoxome, a robust phenotype-driven model that adopts a network-based approach to facilitate automated variant prioritization...
January 9, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30622331/duplication-of-10q24-locus-broadening-the-clinical-and-radiological-spectrum
#9
Muriel Holder-Espinasse, Aleksander Jamsheer, Fabienne Escande, Joris Andrieux, Florence Petit, Anna Sowinska-Seidler, Magdalena Socha, Anna Jakubiuk-Tomaszuk, Marion Gerard, Michèle Mathieu-Dramard, Valérie Cormier-Daire, Alain Verloes, Annick Toutain, Ghislaine Plessis, Philippe Jonveaux, Clarisse Baumann, Albert David, Chantal Farra, Estelle Colin, Sébastien Jacquemont, Annick Rossi, Sahar Mansour, Neeti Ghali, Anne Moncla, Nayana Lahiri, Jane Hurst, Elena Pollina, Christine Patch, Joo Wook Ahn, Anne-Sylvie Valat, Aurélie Mezel, Philippe Bourgeot, David Zhang, Sylvie Manouvrier-Hanu
Split-hand-split-foot malformation (SHFM) is a rare condition that occurs in 1 in 8500-25,000 newborns and accounts for 15% of all limb reduction defects. SHFM is heterogeneous and can be isolated, associated with other malformations, or syndromic. The mode of inheritance is mostly autosomal dominant with incomplete penetrance, but can be X-linked or autosomal recessive. Seven loci are currently known: SHFM1 at 7q21.2q22.1 (DLX5 gene), SHFM2 at Xq26, SHFM3 at 10q24q25, SHFM4 at 3q27 (TP63 gene), SHFM5 at 2q31 and SHFM6 as a result of variants in WNT10B (chromosome 12q13)...
January 8, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30622330/genetic-architecture-of-laterality-defects-revealed-by-whole-exome-sequencing
#10
Alexander H Li, Neil A Hanchard, Mahshid Azamian, Lisa C A D'Alessandro, Zeynep Coban-Akdemir, Keila N Lopez, Nancy J Hall, Heather Dickerson, Annarita Nicosia, Susan Fernbach, Philip M Boone, Tomaz Gambin, Ender Karaca, Shen Gu, Bo Yuan, Shalini N Jhangiani, HarshaVardhan Doddapaneni, Jianhong Hu, Huyen Dinh, Joy Jayaseelan, Donna Muzny, Seema Lalani, Jeffrey Towbin, Daniel Penny, Charles Fraser, James Martin, James R Lupski, Richard A Gibbs, Eric Boerwinkle, Stephanie M Ware, John W Belmont
Aberrant left-right patterning in the developing human embryo can lead to a broad spectrum of congenital malformations. The causes of most laterality defects are not known, with variants in established genes accounting for <20% of cases. We sought to characterize the genetic spectrum of these conditions by performing whole-exome sequencing of 323 unrelated laterality cases. We investigated the role of rare, predicted-damaging variation in 1726 putative laterality candidate genes derived from model organisms, pathway analyses, and human phenotypes...
January 8, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30622329/towards-establishing-consistency-in-triage-in-a-tertiary-specialty
#11
Terri Patricia McVeigh, Deirdre Donnelly, Maryam Al Shehhii, Elizabeth A Jones, Alexandra Murray, Sarah Wedderburn, Mary Porteous, Sally Ann Lynch
Clinical Genetics services provide a diagnostic, counselling and genetic testing service for children and adults affected by, or at risk of, a genetic condition, most of which are rare, and/or genetically heterogeneous. Appropriate triage of referrals is crucial to ensure that the most urgent referrals are seen as quickly as possible, without negatively impacting the waiting times of less urgent cases. We aimed to examine triage practice in six Clinical Genetic centres across the United Kingdom and Ireland...
January 8, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30622328/return-of-individual-genomic-research-results-are-laws-and-policies-keeping-step
#12
Adrian Thorogood, Gratien Dalpé, Bartha Maria Knoppers
Efforts are underway to harmonise the return of individual results and incidental findings from whole genome sequencing (WGS) across research contexts and countries. We reviewed international, regional and national laws and policies applying to return across 20 countries to identify areas of convergence and divergence. Discrepancies between laws and policies are most problematic where they cannot be reconciled through harmonisation of project-level governance. Rules for the return of results apply at different levels in different jurisdictions (e...
January 8, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30622327/an-amish-founder-variant-consolidates-disruption-of-cep55-as-a-cause-of-hydranencephaly-and-renal-dysplasia
#13
Lettie E Rawlins, Hannah Jones, Olivia Wenger, Myat Aye, James Fasham, Gaurav V Harlalka, Barry A Chioza, Alexander Miron, Sian Ellard, Matthew Wakeling, Andrew H Crosby, Emma L Baple
The centrosomal protein 55 kDa (CEP55 (OMIM 610000)) plays a fundamental role in cell cycle regulation and cytokinesis. However, the precise role of CEP55 in human embryonic growth and development is yet to be fully defined. Here we identified a novel homozygous founder frameshift variant in CEP55, present at low frequency in the Amish community, in two siblings presenting with a lethal foetal disorder. The features of the condition are reminiscent of a Meckel-like syndrome comprising of Potter sequence, hydranencephaly, and cystic dysplastic kidneys...
January 8, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30622326/biallelic-sequence-variants-in-ints1-in-patients-with-developmental-delays-cataracts-and-craniofacial-anomalies
#14
Max Krall, Stephanie Htun, Rhonda E Schnur, Alice S Brooks, Laura Baker, Alejandra de Alba Campomanes, Ryan E Lamont, Karen W Gripp, Dina Schneidman-Duhovny, A Micheil Innes, Grazia M S Mancini, Anne M Slavotinek
The Integrator complex subunit 1 (INTS1) is a component of the integrator complex that comprises 14 subunits and associates with RPB1 to catalyze endonucleolytic cleavage of nascent snRNAs and assist RNA polymerase II in promoter-proximal pause-release on protein-coding genes. We present five patients, including two sib pairs, with biallelic sequence variants in INTS1. The patients manifested absent or severely limited speech, an abnormal gait, hypotonia and cataracts. Exome sequencing revealed biallelic variants in INTS1 in all patients...
January 8, 2019: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30573803/a-tyrosine-kinase-activating-variant-asn666ser-in-pdgfrb-causes-a-progeria-like-condition-in-the-severe-end-of-penttinen-syndrome
#15
Cecilie Bredrup, Tomasz Stokowy, Julie McGaughran, Samuel Lee, Dipak Sapkota, Ileana Cristea, Linda Xu, Kåre Steinar Tveit, Gunnar Høvding, Vidar Martin Steen, Eyvind Rødahl, Ove Bruland, Gunnar Houge
Missense variants located to the "molecular brake" in the tyrosine kinase hinge region of platelet-derived growth factor receptor-β, encoded by PFGFRB, can cause Penttinen-type (Val665Ala) and Penttinen-like (Asn666His) premature ageing syndromes, as well as infantile myofibromatosis (Asn666Lys and Pro660Thr). We have found the same de novo PDGFRB c.1997A>G p.(Asn666Ser) variants in two patients with lipodystrophy, acro-osteolysis and severely reduced vision due to corneal neovascularisation, reminiscent of a severe form of Penttinen syndrome with more pronounced connective tissue destruction...
December 20, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30573802/communication-about-genetic-testing-with-breast-and-ovarian-cancer-patients-a-scoping-review
#16
REVIEW
Chris Jacobs, Christine Patch, Susan Michie
Genetic testing of patients with cancer is increasingly offered to guide management, resulting in a growing need for oncology health professionals to communicate genetics information and facilitate informed decision-making in a short time frame. This scoping review aimed to map and synthesise what is known about health professionals' communication about genetic testing for hereditary breast and ovarian cancer with cancer patients. Four databases were systematically searched using a recognised scoping review method...
December 20, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30573801/choosing-not-to-know-accounts-of-non-engagement-with-pre-symptomatic-testing-for-machado-joseph-disease
#17
Álvaro Mendes, Milena Paneque, Angus Clarke, Jorge Sequeiros
This paper reports accounts from people at-risk for, or affected by, Machado-Joseph disease, and their family members, about their decisions not to seek pre-symptomatic testing, therefore remaining (for the time) uninformed about their genetic status. We draw on individual and family semi-structured interviews with participants recruited through a national patient's association (n = 25). Qualitative thematic analysis revealed three main categories of accounts: (1) justifying the decision "not to know", because either no clinical benefit was expected or predictive knowledge was anticipated as psychologically burdensome; (2) prioritizing everyday life, maintaining hope and the goal of living a valid life; and (3) the wish to know: ambivalence and conflict within the family...
December 20, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30573800/a-game-of-hide-and-seq-identification-of-parallel-y-str-evolution-in-deep-rooting-pedigrees
#18
Sofie Claerhout, Michiel Van der Haegen, Lisa Vangeel, Maarten H D Larmuseau, Ronny Decorte
Short tandem repeats on the Y-chromosome (Y-STRs) are common DNA polymorphisms useful for genetic genealogy, population and evolutionary genetics, human genetics, pathology and forensic sciences. It is important to identify all Y-STR variants and to have knowledge of Y-STR mutation rates in order to correctly estimate the time to the most recent common ancestor (tMRCA) between paternally related individuals. When capillary electrophoresis (CE) is performed to analyze genealogical pairs, Y-STR sequence variations remain hidden when the number of repeats is identical...
December 20, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30568244/bone-morphogenetic-protein-4-bmp4-loss-of-function-variant-associated-with-autosomal-dominant-stickler-syndrome-and-renal-dysplasia
#19
Thomas R W Nixon, Allan Richards, Laura K Towns, Gavin Fuller, Stephen Abbs, Philip Alexander, Annie McNinch, Richard N Sandford, Martin P Snead
Stickler syndrome is a genetic disorder that can lead to joint problems, hearing difficulties and retinal detachment. Genes encoding collagen types II, IX and XI are usually responsible, but some families have no causal variant identified. We investigate a variant in the gene encoding growth factor BMP4 in a family with Stickler syndrome with associated renal dysplasia. Next generation sequencing of the coding region of COL2A1, COL11A1 and a panel of genes associated with congenital anomalies of the kidney and urinary tract (CAKUT) was performed...
December 19, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30568243/diaspora-migration-and-the-sciences-a-new-integrated-perspective
#20
REVIEW
Leonard Rutgers, Harry Ostrer, Tracy Prowse, Hannes Schroeder
No abstract text is available yet for this article.
December 19, 2018: European Journal of Human Genetics: EJHG
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